Rants, raves (and occasionally considered opinions) on phyloinformatics, taxonomy, and biodiversity informatics. For more ranty and less considered opinions, see my Twitter feed.ISSN 2051-8188 View this blog in Magazine View.

Wednesday, November 11, 2009

Tag trees: displaying the taxonomy of names in BHL

I've added a feature to my Biodiversity Heritage Library viewer that should help make sense of the names found on a page. Until now I've displayed them as a list of "tags", which ignores the relations among the names. Based on some code I'd developed for my e-Biosphere 09 challenge entry I've added a "tag tree" that displays the classification of the names found on a BHL page:

The idea is that a set of names can make much more sense if you know what kind of organism they are referring to. For example, I don't know what Onetes is, but if I look at BHL page 2298380 I can see that it's an insect:

The names in gray don't occur on the page, but do occur in the tree that links those names (the latter are highlighed in black). The tag tree can be useful for separating out host and parasite, e.g. BHL page 2298491 is about a flea and it's mammalian hosts:

The tag tree can also flag names that might be mistaken, such as those found on page 2298330:

This page has names of some grasshoppers from Madagascar, as well as the name of a butterfly (Tsaratanana), which seems a little odd. Looking at the text, we discover that "Tsaratanana" is Mont. Tsaratanana a mountain in Madagascar. It would be fun to develop tools to annotate such cases so that somebody looking for the butterfly won't be presented with this page.

How it works

The inspiration for this tag tree came from several sources. David Remsen has often used an example of finding a fly name in the middle of a book on birds as being of interest, and the NCBI have a subtree view of taxa in a PubMed article. My own tag tree is constructed by finding for each name the ancestor-descendant path in a local, modified copy of the Catalogue of Life database, then assembling those paths into a tree. Because not all the names on a BHL page are in the Catalogue of Life, there may be names that aren't classified. These are simply listed below the tag tree (see image above).